Hello!
I am rerunning some bulk samples thru my pipeline, but am including more samples from various organs of individuals from either sex and also considering symbiotic state. My All.coldata
looks like this:
> All.coldata
Seq.Batch Symbiotic.State Tissue.Type Sex
FS11_WBL 2 SYM WBL F
FS13_WBL 1 SYM WBL F
FS15_WBL 1 SYM WBL F
FT21_WBL 2 SYM WBL F
FU3_WBL 2 SYM WBL F
MS4_WBL 1 SYM WBL M
MT13_WBL 2 SYM WBL M
MT14_WBL 2 SYM WBL M
MT20_WBL 2 SYM WBL M
MT8_WBL 2 SYM WBL M
FS13_OLL 1 SYM OLL F
FS15_OLL 1 SYM OLL F
FU3_OLL 2 SYM OLL F
MS3_OLL 1 SYM OLL M
MS4_OLL 1 SYM OLL M
MT8_OLL 2 SYM OLL M
FS15_CB 1 SYM CB F
FT12_CB 2 SYM CB F
FU3_CB 2 SYM CB F
MT13_CB 2 SYM CB M
MT6_CB 2 SYM CB M
MT8_CB 2 SYM CB M
FSJM26_WB 2 APO WB F
FSJM61_WB 2 APO WB F
FSJM63_WB 2 APO WB F
FS11_MNTL_190922 2 SYM MNTL F
FU3_MNTL_190931 2 SYM MNTL F
MS3_MNTL 1 SYM MNTL M
MS4_MNTL 2 SYM MNTL M
MT13_MNTL_190910 2 SYM MNTL M
And I'm wondering how best to set up my dds. I've run an analysis before where I consider just Tissue.Type, but I want to think about how sex and symbioses plays a part in the DE as well. Should I run DESeq just comparing tissue.type then add in the design(ddsMF) <- formula(~ type + condition)
for multi-factor design and include the other columns of my All.coldata
?
Please let me know what you think, thanks!
And my sessioninfo()
is:
> sessionInfo()
R version 4.2.2 (2022-10-31)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 11.7.8
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.2.2 fastmap_1.1.1 Matrix_1.5-4 limma_3.54.2 cli_3.6.1
[6] htmltools_0.5.6 tools_4.2.2 rstudioapi_0.15.0 yaml_2.3.7 rmarkdown_2.24
[11] grid_4.2.2 knitr_1.43 xfun_0.40 digest_0.6.33 rlang_1.1.1
[16] evaluate_0.21 lattice_0.21-8
thanks, will do! we work with a non-model organism, but perhaps the folks who do our genomics/sequencing have some input.